scopy.ScoTox package


Created on Fri May 15 22:47:38 2020

A module used for sceening toxicity related substructure.

You can freely use and distribute it. If you have any problem, you could contact with us timely.

@Author: Zhi-Jiang Yang, Dong-Sheng Cao.

@Institution: CBDD Group, Xiangya School of Pharmaceutical Science, CSU, China.

@Homepage: http://www.scbdd.com

@Mail: kotori@cbdd.me and oriental-cds@163.com


Submodules

scopy.ScoTox.tox_filter module

the tool to check molecule whether matched toxicity endpoints.

scopy.ScoTox.tox_filter.Check_Acute_Aquatic_Toxicity(mol, detail=False, showSMILES=False)[source]

Check molecule under Acute_Aquatic_Toxicity Filter, which presents a compound may cause toxicity to liquid(water). There are 99 SMARTS in this endpoint.

Reference:
  1. Hermens, J. L. (1990);

  2. Verhaar, Henk JM, Cees J. Van Leeuwen (1992).

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – The molecule to be scanned

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘Endpoint’, otherwise ‘MatchedAtoms’ and ‘MatchedNames’ are also provided.

Return type

namedtuple

scopy.ScoTox.tox_filter.Check_Biodegradable(mol, detail=False, showSMILES=False)[source]

Check molecule under Biodegradable Filter, which presents a compound may be Biodegradable. There are 9 SMARTS in this enpoint

Reference:
  1. Existing Substances Program (CD-ROM), released April, 2004 (2003).

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – The molecule to be scanned

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘Endpoint’, otherwise ‘MatchedAtoms’ and ‘MatchedNames’ are also provided.

Return type

namedtuple

scopy.ScoTox.tox_filter.Check_Genotoxic_Carcinogenicity_Mutagenicity(mol, detail=False, showSMILES=False)[source]

Check molecule under Developmental_Mitochondrial Filter, which presents a compound may cause carcinogenicity or(and) mutagenicity through genotoxic mechanisms. There are 117 SMARTS in this endpoint.

Reference:
  1. Benigni, Romualdo and Cecilia Bossa. (2008);

  2. Ashby, John and Raymond W. Tennant. (1988);

  3. Kazius, Jeroen, Ross McGuire, Roberta Bursi. (2005);

  4. Bailey, Allan B. (2005).

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – The molecule to be scanned

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘Endpoint’, otherwise ‘MatchedAtoms’ and ‘MatchedNames’ are also provided.

Return type

namedtuple

scopy.ScoTox.tox_filter.Check_LD50_Oral(mol, detail=False, showSMILES=False)[source]

Check molecule under LD50_Oral Filter, which presents a compound may cause acute toxicity during oral administration; There are 20 SMARTS in this endpoint.

Reference:
  1. Tinkov OV (2019).

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – The molecule to be scanned

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘Endpoint’, otherwise ‘MatchedAtoms’ and ‘MatchedNames’ are also provided.

Return type

namedtuple

scopy.ScoTox.tox_filter.Check_NTD(mol, detail=False, showSMILES=False)[source]

Brenk has proposed 105 unwanted groups in HTS

Reference:
  1. Brenk, Ruth (2008).

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – The molecule to be scanned

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘Endpoint’, otherwise ‘MatchedAtoms’ and ‘MatchedNames’ are also provided.

Return type

namedtuple

scopy.ScoTox.tox_filter.Check_NonBiodegradable(mol, detail=False, showSMILES=False)[source]

Check molecule under NonBiodegradable Filter, which presents a compound may be non-biodegradable. There are 19 SMARTS in this enpoint.

Reference:
  1. Environment Canada. Existing Substances Program (CD-ROM), released April, 2004 (2003).

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – The molecule to be scanned

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘Endpoint’, otherwise ‘MatchedAtoms’ and ‘MatchedNames’ are also provided.

Return type

namedtuple

scopy.ScoTox.tox_filter.Check_NonGenotoxic_Carcinogenicity(mol, detail=False, showSMILES=False)[source]

Check molecule under NonGenotoxic_Carcinogenicity Filter, which presents a compound may cause carcinogenicity or(and) mutagenicity through genotoxic mechanisms。 There are 23 SMARTS in this endpoint.

Reference:
  1. Benigni, Romualdo and Cecilia Bossa (2008);

  2. Benigni, Romualdo, Cecilia Bossa and Olga Tcheremenskaia (2013).

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – The molecule to be scanned

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘Endpoint’, otherwise ‘MatchedAtoms’ and ‘MatchedNames’ are also provided.

Return type

namedtuple

scopy.ScoTox.tox_filter.Check_Potential_Electrophilic(mol, detail=False, showSMILES=False)[source]

Check molecule under Potential_Electrophilic Filter, which presents a compound would be more probably take part in electrophilic reaction, and the electrophilic reaction is strongly assosiated with protein binding. There are 119 SMARTS in this endpoint.

Reference:
  1. Enoch, S. J (2011).

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – The molecule to be scanned

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘Endpoint’, otherwise ‘MatchedAtoms’ and ‘MatchedNames’ are also provided.

Return type

namedtuple

scopy.ScoTox.tox_filter.Check_Skin_Sensitization(mol, detail=False, showSMILES=False)[source]

Check molecule under Skin_Sensitization Filter, There are 155 SMARTS in this endpoint.

Reference:
  1. Payne, M. P. and P. T. Walsh (1994).

  2. Enoch, S. J., J. C. Madden and M. T. D. Cronin (2008).

  3. Barratt, M. D (1994).

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – The molecule to be scanned

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘Endpoint’, otherwise ‘MatchedAtoms’ and ‘MatchedNames’ are also provided.

Return type

namedtuple

scopy.ScoTox.tox_filter.Check_SureChEMBL(mol, detail=False, showSMILES=False)[source]

Check molecule under SureChEMBL Filter, which presents a compound would match one or more structural alerts and hence considered to have a MedChem unfriendly status. There are 164 SMARTS in this endpoint.

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – The molecule to be scanned

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘Endpoint’, otherwise ‘MatchedAtoms’ and ‘MatchedNames’ are also provided.

Return type

namedtuple

scopy.ScoTox.tox_filter.Check_Toxicophores(mol, detail=False, showSMILES=False)[source]

There 154 SMARTS in Toxicophres

Parameters
  • mol (rdkit.Chem.rdchem.Mol) – The molecule to be scanned

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘Endpoint’, otherwise ‘MatchedAtoms’ and ‘MatchedNames’ are also provided.

Return type

namedtuple

class scopy.ScoTox.tox_filter.Filter(endpoint, detail=False, showSMILES=False)[source]

Bases: object

Internal Use Only the tool to check molecule(s) whether matched some unexpected endpoints. based on module SmartProcess

Parameters
  • endpoint (str) – The name of endpoint for scanning molecule

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Returns

Result after scanning. If detail has been set to False, only return ‘Disposed’ and ‘Endpoint’, otherwise ‘MatchedAtoms’ and ‘MatchedNames’ are also provided.

Return type

namedtuple

get_pattl()[source]
scan(mol)[source]

scopy.ScoTox.tox_filter_Lib module

class scopy.ScoTox.tox_filter_Lib.Toxfilter(mols, n_jobs=1, detail=False, showSMILES=False)[source]

Bases: object

Here, we comdat the whole function from module tox_fileter for screening molecule library

Parameters
  • mols (Iterable object, each element is rdkit.Chem.rdchem.Mol) – the molecule to be scanned.

  • n_jobs (int, optional) – The number of CPUs to use to do the computation, defaults to 1

  • detail (bool, optional) – Control returning specific infomation or not, defaults to False

  • showSMILES (bool, optional) – Control returning SMILES or not, defaults to False

Check_Acute_Aquatic_Toxicity()[source]

Check molecule under Acute_Aquatic_Toxicity Filter, which presents a compound may cause toxicity to liquid(water). There are 99 SMARTS in this endpoint.

Returns

a list of dictionary

Return type

list

Check_Biodegradable()[source]

Check molecule under Biodegradable Filter, which presents a compound may be Biodegradable. There are 9 SMARTS in this enpoint

Returns

a list of dictionary

Return type

list

Check_Genotoxic_Carcinogenicity_Mutagenicity()[source]

Check molecule under Developmental_Mitochondrial Filter, which presents a compound may cause carcinogenicity or(and) mutagenicity through genotoxic mechanisms. There are 117 SMARTS in this endpoint.

Returns

a list of dictionary

Return type

list

Check_LD50_Oral()[source]

Check molecule under LD50_Oral Filter, which presents a compound may cause acute toxicity during oral administration; There are 20 SMARTS in this endpoint.

Returns

a list of dictionary

Return type

list

Check_NTD(detail=False)[source]

Brenk has proposed 105 unwanted groups in HTS

Returns

a list of dictionary

Return type

list

Check_NonBiodegradable()[source]

Check molecule under NonBiodegradable Filter, which presents a compound may be non-biodegradable. There are 19 SMARTS in this enpoint.

Returns

a list of dictionary

Return type

list

Check_NonGenotoxic_Carcinogenicity()[source]

Check molecule under NonGenotoxic_Carcinogenicity Filter, which presents a compound may cause carcinogenicity or(and) mutagenicity through genotoxic mechanisms。 There are 23 SMARTS in this endpoint.

Returns

a list of dictionary

Return type

list

Check_Potential_Electrophilic()[source]

Check molecule under Potential_Electrophilic Filter, which presents a compound would be more probably take part in electrophilic reaction, and the electrophilic reaction is strongly assosiated with protein binding. There are 119 SMARTS in this endpoint.

Returns

a list of dictionary

Return type

list

Check_Skin_Sensitization()[source]

Check molecule under Skin_Sensitization Filter, There are 155 SMARTS in this endpoint.

Returns

a list of dictionary

Return type

list

Check_SureChEMBL()[source]

Check molecule under SureChEMBL Filter, which presents a compound would match one or more structural alerts and hence considered to have a MedChem unfriendly status. There are 164 SMARTS in this endpoint.

Returns

a list of dictionary

Return type

list

Check_Toxicophores()[source]

There 154 SMARTS in Toxicophres

Returns

a list of dictionary

Return type

list

Module contents

Created on Fri May 15 21:38:08 2020

@Author: Zhi-Jiang Yang, Dong-Sheng Cao @Institution: CBDD Group, Xiangya School of Pharmaceutical Science, CSU, China @Homepage: http://www.scbdd.com @Mail: yzjkid9@gmail.com; oriental-cds@163.com @Blog: https://blog.iamkotori.com